isatty is used by the lexer to determine if the input stream is a terminal or a pipe/file. The lexer uses this information to change its caching behavior (the lexer reads large chunks of the input when it is not a terminal). If you know that your program will never be used in an interactive kind, you can add %option never-interactive to you lexer. When the program is run with user input, use %option interactive. When both uses are desired, you can either generate an interactive lexer, which gives a performance loss when used in batch mode, or provide your own isatty function.